Amarantha - lovely and soft. Makes me think of golden fields of grain. Too soft next to Aphrodite?Amoret - This would be too much of a love-fest with Aphrodite, imo. Maybe in the middle.Atalanta - Fierce and ocean-spacious. Requires you to slow down a bit to say it though.
Bellicent - Makes me think of “bellicose.” Not my favorite.
Belphoebe - Bien sûr.Boudicca - How patriotic, and bodacious. Definitely an aggressive name to my ears, but that’s not necessarily a bad thing.Callisto - I just associate this name with Zeus-rape... and the Ursa constellations too of course which almost makes up for it. I prefer Ursula or Orsa.Ceridwen - Ooh you are going to have a winter babe aren’t you!Circe - Circe and Aphrodite would make a delectable pair.Eulalia - Only if she comes out yodeling.
Euphrosyne - The graces sort of play second fiddle to Aphrodite...Fiammetta - Yes please.
Florimell - Did ChuckJones ever do a Faerie Queene? When I hear this name for some reason I am picturing Daffy Duck in an Elizabethan ruff.Genoveva - Can I interest you in Genovefa?Godiva - Very in-your-face, but I think it’s fabulous, esp w/Aphrodite.
Gwenllian - Gwenllian melts my heart. So beautiful.
Hespera - I feel like you’d know if you had a Hespera once she was born. Such a particular, night-blooming cereus kind of name.Hypatia - Neato. I like this. A bit hard-edged but handsome.
Liriope - Strikes me as an odd plant to exalt in a name, so grassy and sensible, but if it moves you...
Lyonesse - I like this as a middle. Somehow feels related to Aphrodite’s Illyria.
Melpomene - Such a beautiful, cheerful sound. I like this.Melusine - Starbucks
Messalina - Save for a cat.Morgana - Yes. Witchy as all get-out, but good.
Niniane - Yes, but would you feel compelled to carry on with 4-syllable, ee-ending names?Olympia - This would be spot-on as a sis to Aphro-D.Oriana - Not my favorite. Close to Ariana, which I associate with Long Island girls with lots of hairspray and frosted lipstick. Pandora - I feel like Pandora really gets the fuzzy end of the lollypop next to Aphrodite.
Polyhymnia - Polly is such a fun nickname, but Polyhymnia sounds a bit technical to me, like a musical form.Roxana - Roxana and Roo would be delicious.Selene - Not enough oomph next to Aphrodite.Tanaquil - I think first of the beautiful and tragic Tanaquil LeClerq, and then of some kind of imaginary sleep medicine.Titania - When paired with Aphrodite, both become suddenly princessy.Xenia - Yes yes love Xenia.Zenobia - Absolutely.

I won't comment on all your middles (so many beauties!) Here are the ones I'd nix:

Argante - Elegant and Arthurian, but it is very close to “argent.” I think money before the color silver, but then I don’t really speak French.
Bastet - Bastard-ette?
Cissea - Can I interest you in Cassia or Keziah?
Elbereth - a very nice LOTR choice, but I prefer Tinuviel.
Lisanor - Of L-named Arthurian ladies, I prefer Luned and Laudine. Lisanor is so obscure, and nearly contains “snore.”
Oenone - Oenone you di‘int.
Ursaly - Ursula!!

Congrats, how exciting! I LOVE Belphoebe as a sister to Aphrodite. So perfect! Both are overflowing with beauty, neither outshines the other, both have sweet nicknames, they go so well together without being theme-y or too match-y at all. (I like Amoret a lot, but definitely not with Aphrodite. Way over the top romantic.)

I enjoy most of your other options too (except Polyhymnia and Tanaquil, the first sounds like a disorder of some sort, like polyhydramnios, and the latter sounds like a medication, either of which would be unfortunate next to the glorious Aphrodite), especially Hespera, Fiammetta, and Olympia. LoveAmarantha, but not sure if it's too close to Aphrodite? Maybe not...it's so lovely, and not extremely similar...Zenobia isn't one I'm usually fond of, but I like it with Aphrodite. (Zipporah would be gorgeous, too, if it's not too biblical for you!) Belphoebe is definitely my favorite, though!

Oh how exciting! As Roo's name is so impressive, her sister will certainly need a distinctive name in her own right. From your list of your first names, I think these best embody that distinctive and majestic quality that the name for baby girl #2 should have:

I agree with Sessha - it's so cool to be naming another child of yours again so soon! Unfortunately, I don't think I'm much help on your naming threads because your names, while beautiful, aren't really my style. Also, I don't know much background on the mythological-type names. However, I'll make an attempt at dividing your list into "love" and "love not so much" categories:

As an introductory salvo, I'd say that with a sister named Aphrodite, I would be very leery of #2 having any Greek name whatsoever, but particularly a mythological name. And, as you said, I would avoid names of major deities from other pantheons, too. Otherwise you risk a "boxed set" syndrome. Since you're hoping for a large family, many of these choices would be wonderful farther down the line when they can shine instead of looking like beads on a string.

I left Hypatia because Hypatia was a real person and such a kickass namesake I think it deserves to stay on the list.

Titania = large, titanic, etc; not so flattering
Messalina = just don't care for the opera, nor the namesake. She slept with half of Rome, conspired to kill her husband, and was executed. Hmm.Boudicca = everyone will see/day "DICK-a"Tanaquil = sounds like a sleep aid (Nyquil), despite being a good historical namesake. Do you like her other epithets like Cyrilla?Melusine = still a monster, albeit one with a beautiful name. Aphrodite & Melusine? Conflicting imagery?